forked from D-Net/dnet-hadoop
result pids (new xpaths + IS vocabularies)
This commit is contained in:
parent
d6aada4957
commit
093f1aff03
|
|
@ -10,10 +10,27 @@ import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.listFields;
|
|||
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.oaiIProvenance;
|
||||
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier;
|
||||
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty;
|
||||
import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
|
||||
import static eu.dnetlib.dhp.schema.common.ModelConstants.DATASET_DEFAULT_RESULTTYPE;
|
||||
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_ACCESS_MODES;
|
||||
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PID_TYPES;
|
||||
import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PRODUCED_BY;
|
||||
import static eu.dnetlib.dhp.schema.common.ModelConstants.NOT_AVAILABLE;
|
||||
import static eu.dnetlib.dhp.schema.common.ModelConstants.ORP_DEFAULT_RESULTTYPE;
|
||||
import static eu.dnetlib.dhp.schema.common.ModelConstants.OUTCOME;
|
||||
import static eu.dnetlib.dhp.schema.common.ModelConstants.PRODUCES;
|
||||
import static eu.dnetlib.dhp.schema.common.ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE;
|
||||
import static eu.dnetlib.dhp.schema.common.ModelConstants.REPOSITORY_PROVENANCE_ACTIONS;
|
||||
import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT;
|
||||
import static eu.dnetlib.dhp.schema.common.ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE;
|
||||
import static eu.dnetlib.dhp.schema.common.ModelConstants.UNKNOWN;
|
||||
|
||||
import java.util.*;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.Date;
|
||||
import java.util.HashMap;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.Optional;
|
||||
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.dom4j.Document;
|
||||
|
|
@ -47,10 +64,8 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
|
||||
protected static final String DATACITE_SCHEMA_KERNEL_4 = "http://datacite.org/schema/kernel-4";
|
||||
protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3";
|
||||
protected static final Qualifier ORCID_PID_TYPE = qualifier(
|
||||
"ORCID", "Open Researcher and Contributor ID", DNET_PID_TYPES, DNET_PID_TYPES);
|
||||
protected static final Qualifier MAG_PID_TYPE = qualifier(
|
||||
"MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES);
|
||||
protected static final Qualifier ORCID_PID_TYPE = qualifier("ORCID", "Open Researcher and Contributor ID", DNET_PID_TYPES, DNET_PID_TYPES);
|
||||
protected static final Qualifier MAG_PID_TYPE = qualifier("MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES);
|
||||
|
||||
protected static final Map<String, String> nsContext = new HashMap<>();
|
||||
|
||||
|
|
@ -64,8 +79,7 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
nsContext.put("datacite", DATACITE_SCHEMA_KERNEL_3);
|
||||
}
|
||||
|
||||
protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier(
|
||||
"main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
|
||||
protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
|
||||
|
||||
protected AbstractMdRecordToOafMapper(final Map<String, String> code2name) {
|
||||
this.code2name = code2name;
|
||||
|
|
@ -79,20 +93,15 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
.parseText(xml.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3));
|
||||
|
||||
final String type = doc.valueOf("//dr:CobjCategory/@type");
|
||||
final KeyValue collectedFrom = getProvenanceDatasource(
|
||||
doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name");
|
||||
final KeyValue collectedFrom = getProvenanceDatasource(doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name");
|
||||
|
||||
if (collectedFrom == null) {
|
||||
return null;
|
||||
}
|
||||
if (collectedFrom == null) { return null; }
|
||||
|
||||
final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
|
||||
? collectedFrom
|
||||
: getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name");
|
||||
|
||||
if (hostedBy == null) {
|
||||
return null;
|
||||
}
|
||||
if (hostedBy == null) { return null; }
|
||||
|
||||
final DataInfo info = prepareDataInfo(doc);
|
||||
final long lastUpdateTimestamp = new Date().getTime();
|
||||
|
|
@ -107,9 +116,7 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
final String dsId = doc.valueOf(xpathId);
|
||||
final String dsName = doc.valueOf(xpathName);
|
||||
|
||||
if (StringUtils.isBlank(dsId) | StringUtils.isBlank(dsName)) {
|
||||
return null;
|
||||
}
|
||||
if (StringUtils.isBlank(dsId) | StringUtils.isBlank(dsName)) { return null; }
|
||||
|
||||
return keyValue(createOpenaireId(10, dsId, true), dsName);
|
||||
}
|
||||
|
|
@ -125,47 +132,47 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
final List<Oaf> oafs = new ArrayList<>();
|
||||
|
||||
switch (type.toLowerCase()) {
|
||||
case "publication":
|
||||
final Publication p = new Publication();
|
||||
populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||
p.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE);
|
||||
p.setJournal(prepareJournal(doc, info));
|
||||
oafs.add(p);
|
||||
break;
|
||||
case "dataset":
|
||||
final Dataset d = new Dataset();
|
||||
populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||
d.setResulttype(DATASET_DEFAULT_RESULTTYPE);
|
||||
d.setStoragedate(prepareDatasetStorageDate(doc, info));
|
||||
d.setDevice(prepareDatasetDevice(doc, info));
|
||||
d.setSize(prepareDatasetSize(doc, info));
|
||||
d.setVersion(prepareDatasetVersion(doc, info));
|
||||
d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info));
|
||||
d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info));
|
||||
d.setGeolocation(prepareDatasetGeoLocations(doc, info));
|
||||
oafs.add(d);
|
||||
break;
|
||||
case "software":
|
||||
final Software s = new Software();
|
||||
populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||
s.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE);
|
||||
s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info));
|
||||
s.setLicense(prepareSoftwareLicenses(doc, info));
|
||||
s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info));
|
||||
s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info));
|
||||
oafs.add(s);
|
||||
break;
|
||||
case "":
|
||||
case "otherresearchproducts":
|
||||
default:
|
||||
final OtherResearchProduct o = new OtherResearchProduct();
|
||||
populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||
o.setResulttype(ORP_DEFAULT_RESULTTYPE);
|
||||
o.setContactperson(prepareOtherResearchProductContactPersons(doc, info));
|
||||
o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info));
|
||||
o.setTool(prepareOtherResearchProductTools(doc, info));
|
||||
oafs.add(o);
|
||||
break;
|
||||
case "publication":
|
||||
final Publication p = new Publication();
|
||||
populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||
p.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE);
|
||||
p.setJournal(prepareJournal(doc, info));
|
||||
oafs.add(p);
|
||||
break;
|
||||
case "dataset":
|
||||
final Dataset d = new Dataset();
|
||||
populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||
d.setResulttype(DATASET_DEFAULT_RESULTTYPE);
|
||||
d.setStoragedate(prepareDatasetStorageDate(doc, info));
|
||||
d.setDevice(prepareDatasetDevice(doc, info));
|
||||
d.setSize(prepareDatasetSize(doc, info));
|
||||
d.setVersion(prepareDatasetVersion(doc, info));
|
||||
d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info));
|
||||
d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info));
|
||||
d.setGeolocation(prepareDatasetGeoLocations(doc, info));
|
||||
oafs.add(d);
|
||||
break;
|
||||
case "software":
|
||||
final Software s = new Software();
|
||||
populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||
s.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE);
|
||||
s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info));
|
||||
s.setLicense(prepareSoftwareLicenses(doc, info));
|
||||
s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info));
|
||||
s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info));
|
||||
oafs.add(s);
|
||||
break;
|
||||
case "":
|
||||
case "otherresearchproducts":
|
||||
default:
|
||||
final OtherResearchProduct o = new OtherResearchProduct();
|
||||
populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||
o.setResulttype(ORP_DEFAULT_RESULTTYPE);
|
||||
o.setContactperson(prepareOtherResearchProductContactPersons(doc, info));
|
||||
o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info));
|
||||
o.setTool(prepareOtherResearchProductTools(doc, info));
|
||||
oafs.add(o);
|
||||
break;
|
||||
}
|
||||
|
||||
if (!oafs.isEmpty()) {
|
||||
|
|
@ -194,15 +201,9 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
final String projectId = createOpenaireId(40, originalId, true);
|
||||
|
||||
res
|
||||
.add(
|
||||
getRelation(
|
||||
docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info,
|
||||
lastUpdateTimestamp));
|
||||
.add(getRelation(docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, lastUpdateTimestamp));
|
||||
res
|
||||
.add(
|
||||
getRelation(
|
||||
projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info,
|
||||
lastUpdateTimestamp));
|
||||
.add(getRelation(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, lastUpdateTimestamp));
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -247,10 +248,7 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false));
|
||||
r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier")));
|
||||
r.setCollectedfrom(Arrays.asList(collectedFrom));
|
||||
r
|
||||
.setPid(
|
||||
prepareListStructProps(
|
||||
doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info));
|
||||
r.setPid(prepareResultPids(doc, info));
|
||||
r.setDateofcollection(doc.valueOf("//dr:dateOfCollection"));
|
||||
r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation"));
|
||||
r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||
|
|
@ -278,6 +276,8 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
r.setBestaccessright(getBestAccessRights(instances));
|
||||
}
|
||||
|
||||
protected abstract List<StructuredProperty> prepareResultPids(Document doc, DataInfo info);
|
||||
|
||||
private List<Context> prepareContexts(final Document doc, final DataInfo info) {
|
||||
final List<Context> list = new ArrayList<>();
|
||||
for (final Object o : doc.selectNodes("//oaf:concept")) {
|
||||
|
|
@ -358,7 +358,7 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
|
||||
protected abstract Field<String> prepareDatasetStorageDate(Document doc, DataInfo info);
|
||||
|
||||
protected static Qualifier getBestAccessRights(List<Instance> instanceList) {
|
||||
protected static Qualifier getBestAccessRights(final List<Instance> instanceList) {
|
||||
if (instanceList != null) {
|
||||
final Optional<Qualifier> min = instanceList
|
||||
.stream()
|
||||
|
|
@ -398,9 +398,7 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
final String sp = n.valueOf("@sp");
|
||||
final String vol = n.valueOf("@vol");
|
||||
final String edition = n.valueOf("@edition");
|
||||
if (StringUtils.isNotBlank(name)) {
|
||||
return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info);
|
||||
}
|
||||
if (StringUtils.isNotBlank(name)) { return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); }
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
|
@ -453,10 +451,7 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
for (final Object o : node.selectNodes(xpath)) {
|
||||
final Node n = (Node) o;
|
||||
res
|
||||
.add(
|
||||
structuredProperty(
|
||||
n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"),
|
||||
n.valueOf("@schemename"), info));
|
||||
.add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n.valueOf("@schemename"), info));
|
||||
}
|
||||
return res;
|
||||
}
|
||||
|
|
@ -464,9 +459,7 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
protected OAIProvenance prepareOAIprovenance(final Document doc) {
|
||||
final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");
|
||||
|
||||
if (n == null) {
|
||||
return null;
|
||||
}
|
||||
if (n == null) { return null; }
|
||||
|
||||
final String identifier = n.valueOf("./*[local-name()='identifier']");
|
||||
final String baseURL = n.valueOf("./*[local-name()='baseURL']");
|
||||
|
|
@ -481,9 +474,7 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
protected DataInfo prepareDataInfo(final Document doc) {
|
||||
final Node n = doc.selectSingleNode("//oaf:datainfo");
|
||||
|
||||
if (n == null) {
|
||||
return dataInfo(false, null, false, false, REPOSITORY_PROVENANCE_ACTIONS, "0.9");
|
||||
}
|
||||
if (n == null) { return dataInfo(false, null, false, false, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); }
|
||||
|
||||
final String paClassId = n.valueOf("./oaf:provenanceaction/@classid");
|
||||
final String paClassName = n.valueOf("./oaf:provenanceaction/@classname");
|
||||
|
|
@ -495,9 +486,7 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred"));
|
||||
final String trust = n.valueOf("./oaf:trust");
|
||||
|
||||
return dataInfo(
|
||||
deletedbyinference, inferenceprovenance, inferred, false,
|
||||
qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust);
|
||||
return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust);
|
||||
}
|
||||
|
||||
protected Field<String> prepareField(final Node node, final String xpath, final DataInfo info) {
|
||||
|
|
|
|||
|
|
@ -5,7 +5,12 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
|||
|
||||
import java.io.IOException;
|
||||
import java.sql.SQLException;
|
||||
import java.util.*;
|
||||
import java.util.Arrays;
|
||||
import java.util.HashMap;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.Objects;
|
||||
import java.util.Optional;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
|
|
@ -27,7 +32,19 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|||
import eu.dnetlib.dhp.common.DbClient;
|
||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import eu.dnetlib.dhp.schema.oaf.Dataset;
|
||||
import eu.dnetlib.dhp.schema.oaf.Datasource;
|
||||
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
||||
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
||||
import eu.dnetlib.dhp.schema.oaf.Organization;
|
||||
import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
|
||||
import eu.dnetlib.dhp.schema.oaf.Project;
|
||||
import eu.dnetlib.dhp.schema.oaf.Publication;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import eu.dnetlib.dhp.schema.oaf.Software;
|
||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
import scala.Tuple2;
|
||||
|
||||
public class GenerateEntitiesApplication {
|
||||
|
|
@ -39,14 +56,12 @@ public class GenerateEntitiesApplication {
|
|||
public static void main(final String[] args) throws Exception {
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
MigrateMongoMdstoresApplication.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json")));
|
||||
.toString(GenerateEntitiesApplication.class
|
||||
.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json")));
|
||||
|
||||
parser.parseArgument(args);
|
||||
|
||||
Boolean isSparkSessionManaged = Optional
|
||||
final Boolean isSparkSessionManaged = Optional
|
||||
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
|
|
@ -58,17 +73,17 @@ public class GenerateEntitiesApplication {
|
|||
final String dbUrl = parser.get("postgresUrl");
|
||||
final String dbUser = parser.get("postgresUser");
|
||||
final String dbPassword = parser.get("postgresPassword");
|
||||
final String isLookupUrl = parser.get("isLookupUrl");
|
||||
|
||||
final Map<String, String> code2name = loadClassNames(dbUrl, dbUser, dbPassword);
|
||||
final Map<String, String> code2name = loadVocsFromDB(dbUrl, dbUser, dbPassword);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
removeOutputDir(spark, targetPath);
|
||||
generateEntities(spark, code2name, sourcePaths, targetPath);
|
||||
});
|
||||
code2name.putAll(loadVocsFromIS(isLookupUrl));
|
||||
|
||||
final SparkConf conf = new SparkConf();
|
||||
runWithSparkSession(conf, isSparkSessionManaged, spark -> {
|
||||
removeOutputDir(spark, targetPath);
|
||||
generateEntities(spark, code2name, sourcePaths, targetPath);
|
||||
});
|
||||
}
|
||||
|
||||
private static void generateEntities(
|
||||
|
|
@ -77,7 +92,7 @@ public class GenerateEntitiesApplication {
|
|||
final String sourcePaths,
|
||||
final String targetPath) {
|
||||
|
||||
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
final List<String> existingSourcePaths = Arrays
|
||||
.stream(sourcePaths.split(","))
|
||||
.filter(p -> exists(sc, p))
|
||||
|
|
@ -90,27 +105,25 @@ public class GenerateEntitiesApplication {
|
|||
|
||||
for (final String sp : existingSourcePaths) {
|
||||
inputRdd = inputRdd
|
||||
.union(
|
||||
sc
|
||||
.sequenceFile(sp, Text.class, Text.class)
|
||||
.map(k -> new Tuple2<>(k._1().toString(), k._2().toString()))
|
||||
.map(k -> convertToListOaf(k._1(), k._2(), code2name))
|
||||
.filter(Objects::nonNull)
|
||||
.flatMap(list -> list.iterator()));
|
||||
.union(sc
|
||||
.sequenceFile(sp, Text.class, Text.class)
|
||||
.map(k -> new Tuple2<>(k._1().toString(), k._2().toString()))
|
||||
.map(k -> convertToListOaf(k._1(), k._2(), code2name))
|
||||
.filter(Objects::nonNull)
|
||||
.flatMap(list -> list.iterator()));
|
||||
}
|
||||
|
||||
inputRdd
|
||||
.mapToPair(oaf -> new Tuple2<>(ModelSupport.idFn().apply(oaf), oaf))
|
||||
.reduceByKey((o1, o2) -> merge(o1, o2))
|
||||
.map(Tuple2::_2)
|
||||
.map(
|
||||
oaf -> oaf.getClass().getSimpleName().toLowerCase()
|
||||
+ "|"
|
||||
+ OBJECT_MAPPER.writeValueAsString(oaf))
|
||||
.map(oaf -> oaf.getClass().getSimpleName().toLowerCase()
|
||||
+ "|"
|
||||
+ OBJECT_MAPPER.writeValueAsString(oaf))
|
||||
.saveAsTextFile(targetPath, GzipCodec.class);
|
||||
}
|
||||
|
||||
private static Oaf merge(Oaf o1, Oaf o2) {
|
||||
private static Oaf merge(final Oaf o1, final Oaf o2) {
|
||||
if (ModelSupport.isSubClass(o1, OafEntity.class)) {
|
||||
((OafEntity) o1).mergeFrom((OafEntity) o2);
|
||||
} else if (ModelSupport.isSubClass(o1, Relation.class)) {
|
||||
|
|
@ -122,37 +135,41 @@ public class GenerateEntitiesApplication {
|
|||
}
|
||||
|
||||
private static List<Oaf> convertToListOaf(
|
||||
final String id, final String s, final Map<String, String> code2name) {
|
||||
final String id,
|
||||
final String s,
|
||||
final Map<String, String> code2name) {
|
||||
final String type = StringUtils.substringAfter(id, ":");
|
||||
|
||||
switch (type.toLowerCase()) {
|
||||
case "native_oaf":
|
||||
return new OafToOafMapper(code2name).processMdRecord(s);
|
||||
case "native_odf":
|
||||
return new OdfToOafMapper(code2name).processMdRecord(s);
|
||||
case "datasource":
|
||||
return Arrays.asList(convertFromJson(s, Datasource.class));
|
||||
case "organization":
|
||||
return Arrays.asList(convertFromJson(s, Organization.class));
|
||||
case "project":
|
||||
return Arrays.asList(convertFromJson(s, Project.class));
|
||||
case "relation":
|
||||
return Arrays.asList(convertFromJson(s, Relation.class));
|
||||
case "publication":
|
||||
return Arrays.asList(convertFromJson(s, Publication.class));
|
||||
case "dataset":
|
||||
return Arrays.asList(convertFromJson(s, Dataset.class));
|
||||
case "software":
|
||||
return Arrays.asList(convertFromJson(s, Software.class));
|
||||
case "otherresearchproduct":
|
||||
return Arrays.asList(convertFromJson(s, OtherResearchProduct.class));
|
||||
default:
|
||||
throw new RuntimeException("type not managed: " + type.toLowerCase());
|
||||
case "native_oaf":
|
||||
return new OafToOafMapper(code2name).processMdRecord(s);
|
||||
case "native_odf":
|
||||
return new OdfToOafMapper(code2name).processMdRecord(s);
|
||||
case "datasource":
|
||||
return Arrays.asList(convertFromJson(s, Datasource.class));
|
||||
case "organization":
|
||||
return Arrays.asList(convertFromJson(s, Organization.class));
|
||||
case "project":
|
||||
return Arrays.asList(convertFromJson(s, Project.class));
|
||||
case "relation":
|
||||
return Arrays.asList(convertFromJson(s, Relation.class));
|
||||
case "publication":
|
||||
return Arrays.asList(convertFromJson(s, Publication.class));
|
||||
case "dataset":
|
||||
return Arrays.asList(convertFromJson(s, Dataset.class));
|
||||
case "software":
|
||||
return Arrays.asList(convertFromJson(s, Software.class));
|
||||
case "otherresearchproduct":
|
||||
return Arrays.asList(convertFromJson(s, OtherResearchProduct.class));
|
||||
default:
|
||||
throw new RuntimeException("type not managed: " + type.toLowerCase());
|
||||
}
|
||||
}
|
||||
|
||||
private static Map<String, String> loadClassNames(
|
||||
final String dbUrl, final String dbUser, final String dbPassword) throws IOException {
|
||||
private static Map<String, String> loadVocsFromDB(
|
||||
final String dbUrl,
|
||||
final String dbUser,
|
||||
final String dbPassword) throws IOException {
|
||||
|
||||
log.info("Loading vocabulary terms from db...");
|
||||
|
||||
|
|
@ -160,15 +177,13 @@ public class GenerateEntitiesApplication {
|
|||
|
||||
try (DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) {
|
||||
dbClient
|
||||
.processResults(
|
||||
"select code, name from class",
|
||||
rs -> {
|
||||
try {
|
||||
map.put(rs.getString("code"), rs.getString("name"));
|
||||
} catch (final SQLException e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
});
|
||||
.processResults("select code, name from class", rs -> {
|
||||
try {
|
||||
map.put(rs.getString("code"), rs.getString("name"));
|
||||
} catch (final SQLException e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
});
|
||||
}
|
||||
|
||||
log.info("Found " + map.size() + " terms.");
|
||||
|
|
@ -176,6 +191,24 @@ public class GenerateEntitiesApplication {
|
|||
return map;
|
||||
}
|
||||
|
||||
private static Map<String, String> loadVocsFromIS(final String isLookupUrl) throws IOException, ISLookUpException {
|
||||
final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookupUrl);
|
||||
|
||||
final String xquery =
|
||||
IOUtils.toString(GenerateEntitiesApplication.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/xquery/load_vocabularies.xquery"));
|
||||
|
||||
final Map<String, String> map = new HashMap<>();
|
||||
|
||||
for (final String s : isLookUpService.quickSearchProfile(xquery)) {
|
||||
final String[] arr = s.split("@=@");
|
||||
if (arr.length == 4) {
|
||||
map.put(arr[2].trim(), arr[3].trim());
|
||||
}
|
||||
}
|
||||
|
||||
return map;
|
||||
}
|
||||
|
||||
private static Oaf convertFromJson(final String s, final Class<? extends Oaf> clazz) {
|
||||
try {
|
||||
return OBJECT_MAPPER.readValue(s, clazz);
|
||||
|
|
@ -196,7 +229,7 @@ public class GenerateEntitiesApplication {
|
|||
}
|
||||
}
|
||||
|
||||
private static void removeOutputDir(SparkSession spark, String path) {
|
||||
private static void removeOutputDir(final SparkSession spark, final String path) {
|
||||
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -130,8 +130,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
|
|||
|
||||
final Instance instance = new Instance();
|
||||
instance
|
||||
.setInstancetype(
|
||||
prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
|
||||
.setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
|
||||
instance.setCollectedfrom(collectedfrom);
|
||||
instance.setHostedby(hostedby);
|
||||
instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
|
||||
|
|
@ -147,14 +146,13 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
|
|||
|
||||
final List<Node> nodes = Lists.newArrayList(doc.selectNodes("//dc:identifier"));
|
||||
instance
|
||||
.setUrl(
|
||||
nodes
|
||||
.stream()
|
||||
.filter(n -> StringUtils.isNotBlank(n.getText()))
|
||||
.map(n -> n.getText().trim())
|
||||
.filter(u -> u.startsWith("http"))
|
||||
.distinct()
|
||||
.collect(Collectors.toCollection(ArrayList::new)));
|
||||
.setUrl(nodes
|
||||
.stream()
|
||||
.filter(n -> StringUtils.isNotBlank(n.getText()))
|
||||
.map(n -> n.getText().trim())
|
||||
.filter(u -> u.startsWith("http"))
|
||||
.distinct()
|
||||
.collect(Collectors.toCollection(ArrayList::new)));
|
||||
|
||||
return Lists.newArrayList(instance);
|
||||
}
|
||||
|
|
@ -279,15 +277,9 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
|
|||
final String otherId = createOpenaireId(50, originalId, false);
|
||||
|
||||
res
|
||||
.add(
|
||||
getRelation(
|
||||
docId, otherId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info,
|
||||
lastUpdateTimestamp));
|
||||
.add(getRelation(docId, otherId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info, lastUpdateTimestamp));
|
||||
res
|
||||
.add(
|
||||
getRelation(
|
||||
otherId, docId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info,
|
||||
lastUpdateTimestamp));
|
||||
.add(getRelation(otherId, docId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info, lastUpdateTimestamp));
|
||||
}
|
||||
}
|
||||
return res;
|
||||
|
|
@ -297,4 +289,9 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
|
|||
protected Qualifier prepareResourceType(final Document doc, final DataInfo info) {
|
||||
return null; // NOT PRESENT IN OAF
|
||||
}
|
||||
|
||||
@Override
|
||||
protected List<StructuredProperty> prepareResultPids(final Document doc, final DataInfo info) {
|
||||
return prepareListStructProps(doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -120,8 +120,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
|
|||
|
||||
final Instance instance = new Instance();
|
||||
instance
|
||||
.setInstancetype(
|
||||
prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
|
||||
.setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
|
||||
instance.setCollectedfrom(collectedfrom);
|
||||
instance.setHostedby(hostedby);
|
||||
instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
|
||||
|
|
@ -170,10 +169,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
|
|||
&& !dateType.equalsIgnoreCase("Updated")
|
||||
&& !dateType.equalsIgnoreCase("Available")) {
|
||||
res
|
||||
.add(
|
||||
structuredProperty(
|
||||
((Node) o).getText(), "UNKNOWN", "UNKNOWN", DNET_DATA_CITE_DATE, DNET_DATA_CITE_DATE,
|
||||
info));
|
||||
.add(structuredProperty(((Node) o).getText(), "UNKNOWN", "UNKNOWN", DNET_DATA_CITE_DATE, DNET_DATA_CITE_DATE, info));
|
||||
}
|
||||
}
|
||||
return res;
|
||||
|
|
@ -225,16 +221,14 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
|
|||
protected List<Field<String>> prepareOtherResearchProductContactGroups(
|
||||
final Document doc,
|
||||
final DataInfo info) {
|
||||
return prepareListFields(
|
||||
doc, "//datacite:contributor[@contributorType='ContactGroup']/datacite:contributorName", info);
|
||||
return prepareListFields(doc, "//datacite:contributor[@contributorType='ContactGroup']/datacite:contributorName", info);
|
||||
}
|
||||
|
||||
@Override
|
||||
protected List<Field<String>> prepareOtherResearchProductContactPersons(
|
||||
final Document doc,
|
||||
final DataInfo info) {
|
||||
return prepareListFields(
|
||||
doc, "//datacite:contributor[@contributorType='ContactPerson']/datacite:contributorName", info);
|
||||
return prepareListFields(doc, "//datacite:contributor[@contributorType='ContactPerson']/datacite:contributorName", info);
|
||||
}
|
||||
|
||||
@Override
|
||||
|
|
@ -260,8 +254,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
|
|||
protected List<Field<String>> prepareSoftwareDocumentationUrls(
|
||||
final Document doc,
|
||||
final DataInfo info) {
|
||||
return prepareListFields(
|
||||
doc, "//datacite:relatedIdentifier[@relatedIdentifierType='URL' and @relationType='IsDocumentedBy']", info);
|
||||
return prepareListFields(doc, "//datacite:relatedIdentifier[@relatedIdentifierType='URL' and @relationType='IsDocumentedBy']", info);
|
||||
}
|
||||
|
||||
// DATASETS
|
||||
|
|
@ -335,29 +328,16 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
|
|||
|
||||
if (type.equalsIgnoreCase("IsSupplementTo")) {
|
||||
res
|
||||
.add(
|
||||
getRelation(
|
||||
docId, otherId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, collectedFrom, info,
|
||||
lastUpdateTimestamp));
|
||||
.add(getRelation(docId, otherId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, collectedFrom, info, lastUpdateTimestamp));
|
||||
res
|
||||
.add(
|
||||
getRelation(
|
||||
otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, collectedFrom, info,
|
||||
lastUpdateTimestamp));
|
||||
.add(getRelation(otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, collectedFrom, info, lastUpdateTimestamp));
|
||||
} else if (type.equals("IsPartOf")) {
|
||||
|
||||
res
|
||||
.add(
|
||||
getRelation(
|
||||
docId, otherId, RESULT_RESULT, PART, IS_PART_OF, collectedFrom, info,
|
||||
lastUpdateTimestamp));
|
||||
.add(getRelation(docId, otherId, RESULT_RESULT, PART, IS_PART_OF, collectedFrom, info, lastUpdateTimestamp));
|
||||
res
|
||||
.add(
|
||||
getRelation(
|
||||
otherId, docId, RESULT_RESULT, PART, HAS_PARTS, collectedFrom, info,
|
||||
lastUpdateTimestamp));
|
||||
} else {
|
||||
}
|
||||
.add(getRelation(otherId, docId, RESULT_RESULT, PART, HAS_PARTS, collectedFrom, info, lastUpdateTimestamp));
|
||||
} else {}
|
||||
}
|
||||
}
|
||||
return res;
|
||||
|
|
@ -365,8 +345,16 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
|
|||
|
||||
@Override
|
||||
protected Qualifier prepareResourceType(final Document doc, final DataInfo info) {
|
||||
return prepareQualifier(
|
||||
doc, "//*[local-name() = 'resource']//*[local-name() = 'resourceType']", DNET_DATA_CITE_RESOURCE,
|
||||
DNET_DATA_CITE_RESOURCE);
|
||||
return prepareQualifier(doc, "//*[local-name() = 'resource']//*[local-name() = 'resourceType']", DNET_DATA_CITE_RESOURCE, DNET_DATA_CITE_RESOURCE);
|
||||
}
|
||||
|
||||
@Override
|
||||
protected List<StructuredProperty> prepareResultPids(final Document doc, final DataInfo info) {
|
||||
final List<StructuredProperty> res = new ArrayList<>();
|
||||
res.addAll(prepareListStructProps(doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info));
|
||||
res.addAll(prepareListStructProps(doc, "//datacite:identifier[@identifierType != 'URL']", "@identifierType", "dnet:pid_types", "dnet:pid_types", info));
|
||||
res.addAll(prepareListStructProps(doc, "//datacite:alternateIdentifier[@alternateIdentifierType != 'URL']", "@alternateIdentifierType", "dnet:pid_types", "dnet:pid_types", info));
|
||||
return res;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -34,6 +34,11 @@
|
|||
"paramLongName": "postgresPassword",
|
||||
"paramDescription": "postgres password",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "islookup",
|
||||
"paramLongName": "isLookupUrl",
|
||||
"paramDescription": "the url of the ISLookupService",
|
||||
"paramRequired": true
|
||||
}
|
||||
|
||||
]
|
||||
Loading…
Reference in New Issue